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- PDB-1qhn: CHLORAMPHENICOL PHOSPHOTRANSFERASE FROM STREPTOMYCES VENEZUELAE -

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Basic information

Entry
Database: PDB / ID: 1qhn
TitleCHLORAMPHENICOL PHOSPHOTRANSFERASE FROM STREPTOMYCES VENEZUELAE
ComponentsCHLORAMPHENICOL PHOSPHOTRANSFERASE
KeywordsTRANSFERASE / KINASE / ANTIBIOTIC RESISTANCE / PHOSPHORYLATION / MONONUCLEOTIDE BINDING FOLD
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / kinase activity / response to antibiotic / ATP binding
Similarity search - Function
Chloramphenicol phosphotransferase-like / Chloramphenicol phosphotransferase-like protein / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chloramphenicol 3-O phosphotransferase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsIzard, T.
CitationJournal: Embo J. / Year: 2000
Title: The Crystal Structures of Chloramphenicol Phosphotransferase Reveal a Novel Inactivation Mechanism
Authors: Izard, T. / Ellis, J.
History
DepositionMay 23, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHLORAMPHENICOL PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2122
Polymers19,1161
Non-polymers961
Water3,099172
1
A: CHLORAMPHENICOL PHOSPHOTRANSFERASE
hetero molecules

A: CHLORAMPHENICOL PHOSPHOTRANSFERASE
hetero molecules

A: CHLORAMPHENICOL PHOSPHOTRANSFERASE
hetero molecules

A: CHLORAMPHENICOL PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8478
Polymers76,4634
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
crystal symmetry operation26_555-x,-y+1/2,z1
crystal symmetry operation38_555-y+1/4,-x+1/4,-z+1/41
Buried area7630 Å2
ΔGint-130 kcal/mol
Surface area28800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)200.000, 200.000, 200.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-772-

HOH

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Components

#1: Protein CHLORAMPHENICOL PHOSPHOTRANSFERASE / CPT


Mass: 19115.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces venezuelae (bacteria) / Strain: ISP5230
References: UniProt: Q56148, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 8.8 Å3/Da / Density % sol: 86 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
250 mMTris-HCl1drop
30.4 Mammonium sulfate1drop
44 %acetonitrile1drop
55 mMCm1drop
60.1 MTris-HCl1reservoir
71.14 Mammonium sulfate1reservoir
810 mMmagnesium chloride1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785, 0.9783, 0.88
DetectorDetector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97851
20.97831
30.881
ReflectionResolution: 2.7→20 Å / Num. obs: 18936 / % possible obs: 99.5 % / Redundancy: 13.52 % / Biso Wilson estimate: 54.9 Å2 / Rmerge(I) obs: 0.128 / Rsym value: 12.8 / Net I/σ(I): 11.1
Reflection shellResolution: 2.7→2.78 Å / Rmerge(I) obs: 0.368 / Rsym value: 36.8 / % possible all: 100
Reflection
*PLUS
Num. measured all: 255940
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 9801121.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 922 4.9 %RANDOM
Rwork0.201 ---
obs0.201 18929 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.1 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.7→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 5 172 1497
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.011.5
X-RAY DIFFRACTIONc_mcangle_it6.222
X-RAY DIFFRACTIONc_scbond_it8.972
X-RAY DIFFRACTIONc_scangle_it12.692.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 145 4.7 %
Rwork0.24 2916 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER-TOPOLOGY
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69

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